When I recently downloaded el capitan, I tried to copy it to an external HD and in the process, the permissions box disappeared so I emailed shirt-pocket and the reply was to use the help option. It is a comprehensive 60 page list of everything you can think of except how to recover the permission box.
Shirt-Pocket did say he would get back to me but I would like to use superduper now if possible.
Before I downloaded el capitan, superduper always checked permissions but when I tried to transfer el capitan to another HD ( the HD I intended to download to in the first place) permissions didn't appear because I didn't tick the permissions box when it first opened. Before, that box was always ticked but I never noticed that it wasn't, so I thought there was a problem. I think senility is setting in!